Basically we have distributed a database and we want to check for updates made to it and pull an updated version if there is one;

Steps
1) Open database
2) Check for the existence of a file on a specified share
3) If the file exists, open another database and close this one
4) The other database then pulls the new version from the share and then
5) Opens the new version before clocing itself!

Look at Step 3 - Open's another database - it is this one which needs to close immediately if it hasn't been opened from the command line

Whilst the code above helps a little bit towards what we need to do, it doesn't allow me to run a test within the second database to check if it has been opened from a command line of not?

You can use parameters in command line:
"c:\Program Files\Microsoft Office\MSACCESS.EXE" "c:\MyDB.mdb" /cmd 1
In code you can get it with Command:
Dim CmdLine
CmdLine = Trim(Command())
If len(CmdLine) = 0 then docmd.quit

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